3STU

Crystal Structure of tomato Methylketone Synthase I complexed with methyl-3-hydroxydodecanoate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7YAS 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.52770.1M PIPES-Na+, 22% (w/v) PEG 8000, 0.3M NaBr, 2mM dithiothreitol, 2 hr soak in 1mM methyl-3-hydroxydodecanoate, pH 6.5, vapor diffusion, hanging drop, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.652.73

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 48.197α = 90
b = 105.716β = 96.51
c = 59.888γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 325 mm CCD2005-05-31MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL9-20.97946SSRLBL9-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.9339.597.80.06324.73.74467043407-336.59
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.931.9798.70.4990.4993.52875

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT7YAS1.9339.54467043407218697.170.2380.21630.21490.2423RANDOM29.1645
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
-0.010.010.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.864
r_dihedral_angle_3_deg12.943
r_dihedral_angle_4_deg11.222
r_dihedral_angle_1_deg5.179
r_scangle_it1.959
r_scbond_it1.165
r_angle_refined_deg1.042
r_mcangle_it0.939
r_mcbond_it0.495
r_chiral_restr0.071
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.864
r_dihedral_angle_3_deg12.943
r_dihedral_angle_4_deg11.222
r_dihedral_angle_1_deg5.179
r_scangle_it1.959
r_scbond_it1.165
r_angle_refined_deg1.042
r_mcangle_it0.939
r_mcbond_it0.495
r_chiral_restr0.071
r_bond_refined_d0.008
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3969
Nucleic Acid Atoms
Solvent Atoms246
Heterogen Atoms28

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
Blu-Icedata collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing